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Data Update

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Ingy döt Net 2023-07-09 17:42:30 -04:00
parent 015c2add84
commit e50b5c3114
206 changed files with 6337 additions and 523 deletions
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16
Task/Bioinformatics-base-count/Kotlin/bioinformatics-base-count.kotlin
View file

@ -1,13 +1,13 @@
fun printSequence(sequence: String, width: Int = 50) {
fun <K, V> printWithLabel(k: K, v: V) {
val label = k.toString().padStart(5)
println("$label: $v")
}
fun printWithLabel(label: Any, data: Any) =
label.toString().padStart(5).also { println("$it: $data") }
println("SEQUENCE:")
sequence.chunked(width).withIndex().forEach { (i, line) ->
printWithLabel(i*width + line.length, line)
sequence.chunked(width).forEachIndexed() { i, chunk ->
printWithLabel(i * width + chunk.length, chunk)
}
println("BASE:")
sequence.groupingBy { it }.eachCount().forEach { (k, v) ->
printWithLabel(k, v)
@ -17,6 +17,4 @@ fun printSequence(sequence: String, width: Int = 50) {
const val BASE_SEQUENCE = "CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATATTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTATCGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTGTCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGACGACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT"
fun main() {
printSequence(BASE_SEQUENCE)
}
fun main() = printSequence(BASE_SEQUENCE)

67
Task/Bioinformatics-base-count/REXX/bioinformatics-base-count.rexx
View file

@ -1,31 +1,36 @@
/*REXX program finds the number of each base in a DNA string (along with a total). */
parse arg dna .
if dna=='' | dna=="," then dna= 'cgtaaaaaattacaacgtcctttggctatctcttaaactcctgctaaatg' ,
'ctcgtgctttccaattatgtaagcgttccgagacggggtggtcgattctg' ,
'aggacaaaggtcaagatggagcgcatcgaacgcaataaggatcatttgat' ,
'gggacgtttcgtcgacaaagtcttgtttcgagagtaacggctaccgtctt' ,
'cgattctgcttataacactatgttcttatgaaatggatgttctgagttgg' ,
'tcagtcccaatgtgcggggtttcttttagtacgtcgggagtggtattata' ,
'tttaatttttctatatagcgatctgtatttaagcaattcatttaggttat' ,
'cgccgcgatgctcggttcggaccgccaagcatctggctccactgctagtg' ,
'tcctaaatttgaatggcaaacacaaataagatttagcaattcgtgtagac' ,
'gaccggggacttgcatgatgggagcagctttgttaaactacgaacgtaat'
dna= space(dna, 0); upper dna /*elide blanks from DNA; uppercase it. */
say '────────length of the DNA string: ' length(dna)
@.= 0 /*initialize the count for all bases. */
w= 1 /*the maximum width of a base count. */
$= /*a placeholder for the names of bases.*/
do j=1 for length(dna) /*traipse through the DNA string. */
_= substr(dna, j, 1) /*obtain a base name from the DNA str. */
if pos(_, $)==0 then $= $ || _ /*if not found before, add it to list. */
@._= @._ + 1 /*bump the count of this base. */
w= max(w, length(@._) ) /*compute the maximum width number. */
end /*j*/
say
do k=0 for 255; z= d2c(k) /*traipse through all possibilities. */
if pos(z, $)==0 then iterate /*Was this base found? No, then skip. */
say ' base ' z " has a basecount of: " right(@.z, w)
@.tot= @.tot + @.z /*add to a grand total to verify count.*/
end /*k*/ /*stick a fork in it, we're all done. */
say
say '────────total for all basecounts:' right(@.tot, w+1)
/*REXX program finds the number of each base in a DNA string */
/* (along with a total). */
Parse Arg dna .
If dna==''|dna==',' Then
dna='cgtaaaaaattacaacgtcctttggctatctcttaaactcctgctaaatg',
'ctcgtgctttccaattatgtaagcgttccgagacggggtggtcgattctg',
'aggacaaaggtcaagatggagcgcatcgaacgcaataaggatcatttgat',
'gggacgtttcgtcgacaaagtcttgtttcgagagtaacggctaccgtctt',
'cgattctgcttataacactatgttcttatgaaatggatgttctgagttgg',
'tcagtcccaatgtgcggggtttcttttagtacgtcgggagtggtattata',
'tttaatttttctatatagcgatctgtatttaagcaattcatttaggttat',
'cgccgcgatgctcggttcggaccgccaagcatctggctccactgctagtg',
'tcctaaatttgaatggcaaacacaaataagatttagcaattcgtgtagac',
'gaccggggacttgcatgatgggagcagctttgttaaactacgaacgtaat'
dna=translate(space(dna,0)) /* elide blanks from DNA; uppercas*/
Say '--------length of the DNA string: ' length(dna)
count.=0 /* initialize the count for all bases*/
w=1 /* the maximum width of a base count */
names='' /* list of all names */
Do j=1 To length(dna) /* traipse through the DNA string */
name=substr(dna,j,1) /* obtain a base name from the DNA */
If pos(name,names)==0 Then
names=names||name /* if not found, add it to the list */
count.name=count.name+1 /* bump the count of this base. */
w=max(w,length(count.name)) /* compute the maximum number width */
End
Say
Do k=0 To 255
z=d2c(k) /* traipse through all possibilities */
If pos(z,names)>0 Then Do
Say ' base ' z ' has a basecount of: ' right(count.z,w)
count.tot=count.tot+count.z /* add to a grand total to verify */
End
End
Say
Say '--------total for all basecounts:' right(count.tot,w+1)